Graduate School of health and Medical Sciences

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Single-Cell Multiomics: From Wet Lab to Bioinformatics
Provider: Faculty of Health and Medical Sciences

Activity no.: 3214-26-00-00	There are 6 available seats
	Enrollment deadline: 23/02/2026

Date and time	30.03.2026, at: 09:00 - 18.05.2026, at: 16:00
Regular seats	12
Lecturers	Jan Pravsgaard Christensen
ECTS credits	5.50

Contact person	Jan P. Christensen E-mail address: jpc@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration SUND E-mail address: phdkursus@sund.ku.dk

Enrolment guidelines This is a specialised course. This means that 80% of the seats are reserved to PhD students enrolled at the Faculty of Health and Medical Sciences at UCPH and 20% og the seats are reserved to PhD students from other Danish Universities/faculties (except CBS). The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. All other participants must pay the course fee. Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Learning objectives A student who has met the objectives of the course will be able to: 1. Understand the basic principles of Illumina sequencing-by-synthesis (SBS) and the underlying technologies used in single-cell RNA sequencing 2. Perform a full 10x Genomics single-cell RNA-seq wet-lab protocol, from sample QC to library preparation. 3. Execute downstream analysis using command-line tools (Linux, Cell Ranger) and R-based frameworks (Seurat) for quality control, clustering, multimodal integration, and interpretation of single-cell data. 4. Integrate multiomic data including gene expression, CITE-seq, and immune receptor profiling (VDJ). 5. Troubleshoot common pitfalls in both wet-lab protocols and data analysis pipelines. Content The course combines theoretical lectures and hands-on exercises in both wet lab and bioinformatics domains. Students will be guided through the Illumina SBS sequencing technology, single-cell experimental design, and the complete 10x Genomics 3’ GEX v4 workflow. The bioinformatics module will include Linux basics, Cell Ranger, Seurat analysis, multiomic integration, and VDJ interpretation. Participants PhD students and people on similar level, no previous skills in Single-Cell Multiomics are needed. Relevance to graduate programmes The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH: Immunology and Infectious Diseases Language English Form E-learning lectures, practical and theoretical exercises. The course has a follow up where students can get help designing their own experiments. Course director Professor Jan Pravsgaard Christensen, ISIM, 35327873, jpc@sund.ku.dk Teachers Rasmus Borring Klitgaard, PhD, Wet lab and sequencing responsible at the Flow Cytometry & Single Cell Core Facility Farideh Moharrek, PhD, Bioinformaticain at the Flow Cytometry & Single Cell Core Facility Dates 30/3 – 13/4-2026, you are expected to watch e-learning videos at home, and test you self, app 20 hours Wet lab on two of the following dates 13-14/4-26, kl. 9-16 practical exercise in core facility, TEAM 1 15-16/4-26, kl. 9-16 practical exercise in core facility, TEAM 2 20-21/4-26, kl. 9-16 practical exercise in core facility, TEAM 3 Bioinformatics 4/5-26, kl. 9-16 practical exercise in core facility, ALL TEAMS 11/5-26, kl. 9-16 practical exercise in core facility, ALL TEAMS 18/5-26, kl. 9-16 practical exercise in core facility, ALL TEAMS Course location The Panum Institute, Blegdamsvej 3B, DK-2200 Copenhagen N. Maersk Tower, 13th and 14th floor. Registration Please register before 23 February 2026 Expected frequency We will start with one course and evaluate the interest to determine future offerings. Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment. Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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